Prediction of proteasome cleavage sites
yeast proteasome

Yeast proteasome picture- Groll M., et. al. (1997) Nature 386:463 PDB code 1RYP

Proteasomal cleavage of proteins is the first step in the processing of most antigenic peptides that are presented to cytotoxic T cells. Still, its specificity and mechanism are not fully understood. To identify preferred sequence signals that are used for generation of antigenic peptides by the proteasome, we performed a rigorous analysis of the residues at the termini and flanking regions of naturally processed peptides eluted from MHC class I molecules.[Altuvia et. al. 2000] Our results show that both the C terminus (position P1 of the cleavage site) and its immediate flanking position (P1') possess significant signals. The N termini of the peptides show these signals only weakly, consistent with previous findings that antigenic peptides may be cleaved by the proteasome with N-terminal extensions. Nevertheless, we succeed to demonstrate indirectly that the N-terminal cleavage sites contain the same preferred signals at position P1'. The signals found at the P1 and P1' positions of the cleavage site can be translated to a cleavage score which can estimate the cleavage potential of positions along the sequence. nice-cut.tab    scores.html

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